Related papers: Motif matching using gapped patterns
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
A degenerate string is a sequence of sets of characters. A generalized degenerate (GD) string extends this notion to the sequence of sets of strings, where strings of the same set are of equal length. Finding an exact match for a pattern…
Given a text and a pattern over an alphabet, the pattern matching problem searches for all occurrences of the pattern in the text. An equivalence relation $\approx$ is called a substring consistent equivalence relation (SCER), if for two…
Pattern matching is an important feature of programming languages for data abstraction. Many pattern-matching extensions have been proposed and implemented for extending the range of data types to which pattern matching is applicable. Among…
Matching two texts is a fundamental problem in many natural language processing tasks. An effective way is to extract meaningful matching patterns from words, phrases, and sentences to produce the matching score. Inspired by the success of…
We consider how to index strings, trees and graphs for jumbled pattern matching when we are asked to return a match if one exists. For example, we show how, given a tree containing two colours, we can build a quadratic-space index with…
Graph pattern matching is a routine process for a wide variety of applications such as social network analysis. It is typically defined in terms of subgraph isomorphism which is NP-Complete. To lower its complexity, many extensions of graph…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
In this paper, we present a fast and strong neural approach for general purpose text matching applications. We explore what is sufficient to build a fast and well-performed text matching model and propose to keep three key features…
We generalise a multiple string pattern matching algorithm, recently proposed by Fredriksson and Grabowski [J. Discr. Alg. 7, 2009], to deal with arbitrary dictionaries on an alphabet of size $s$. If $r_m$ is the number of words of length…
With the advent of large-scale heterogeneous search engines comes the problem of unified search control resulting in mismatches that could have otherwise avoided. A mechanism is needed to determine exact patterns in web mining and…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
We address the problem of merging graph and feature-space information while learning a metric from structured data. Existing algorithms tackle the problem in an asymmetric way, by either extracting vectorized summaries of the graph…
The trie data structure is a good choice for finite maps whose keys are data structures (trees) rather than atomic values. But what if we want the keys to be patterns, each of which matches many lookup keys? Efficient matching of this kind…
Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper,…
In this paper we describe two simple, fast, space-efficient algorithms for finding all matches of an indeterminate pattern $p = p[1..m]$ in an indeterminate string $x = x[1..n]$, where both $p$ and $x$ are defined on a "small" ordered…
In most computer vision and image analysis problems, it is necessary to define a similarity measure between two or more different objects or images. Template matching is a classic and fundamental method used to score similarities between…
Universal quantifiers occur frequently in proof obligations produced by program verifiers, for instance, to axiomatize uninterpreted functions and to express properties of arrays. SMT-based verifiers typically reason about them via…
String matching is one of the most fundamental problems in computer science. A natural problem is to determine the number of characters that need to be queried (i.e. the decision tree complexity) in a string in order to decide whether this…
In real-world, many problems can be formulated as the alignment between two geometric patterns. Previously, a great amount of research focus on the alignment of 2D or 3D patterns, especially in the field of computer vision. Recently, the…